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Protein Science (2002), 11:2138-2147.
Copyright © 2002 The Protein Society

Active site geometry of oxalate decarboxylase from Flammulina velutipes: Role of histidine-coordinated manganese in substrate recognition

Subhra Chakraborty1, Niranjan Chakraborty1, Deepti Jain2, Dinakar M. Salunke2 and Asis Datta1

1 National Center for Plant Genome Research, Jawaharlal Nehru University Campus, New Delhi 110067, India
2 Structural Biology Unit, National Institute of Immunology, New Delhi 110067, India

Reprint requests to: Asis Datta, National Center for Plant Genome Research, Jawaharlal Nehru University Campus, New Delhi 110067, India; e-mail: asisdatta{at}hotmail.com; fax: 91-011-616-7394.

Oxalate decarboxylase (OXDC) from the wood-rotting fungus Flammulina velutipes, which catalyzes the conversion of oxalate to formic acid and CO2 in a single-step reaction, is a duplicated double-domain germin family enzyme. It has agricultural as well as therapeutic importance. We reported earlier the purification and molecular cloning of OXDC. Knowledge-based modeling of the enzyme reveals a ß-barrel core in each of the two domains organized in the hexameric state. A cluster of three histidines suitably juxtaposed to coordinate a divalent metal ion exists in both the domains. Involvement of the two histidine clusters in the catalytic mechanism of the enzyme, possibly through coordination of a metal cofactor, has been hypothesized because all histidine knockout mutants showed total loss of decarboxylase activity. The atomic absorption spectroscopy analysis showed that OXDC contains Mn2+ at up to 2.5 atoms per subunit. Docking of the oxalate in the active site indicates a similar electrostatic environment around the substrate-binding site in the two domains. We suggest that the histidine coordinated manganese is critical for substrate recognition and is directly involved in the catalysis of the enzyme.

Keywords: Oxalate decarboxylase; ECM protein; germin motif; knowledge-based modeling; knockout mutants


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